Bottom Line:
Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation.Here we review available techniques and future possibilities, arguing that the full potential of single-cell epigenetic studies will be realized through parallel profiling of genomic, transcriptional, and epigenetic information.

ABSTRACTEmerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that the full potential of single-cell epigenetic studies will be realized through parallel profiling of genomic, transcriptional, and epigenetic information.

Fig1: Epigenomics and the spectrum of single-cell sequencing technologies. The diagram outlines the single-cell sequencing technologies currently available. A single cell is first isolated by means of droplet encapsulation, manual manipulation, fluorescence-activated cell sorting (FACS) or microfluidic processing. The first examples of single-cell multi-omic technologies have used parallel amplification or physical separation to measure gene expression (scRNA-seq) and DNA sequence (scDNA-seq) from the same cell. Note that single-cell bisulfite conversion followed by sequencing (scBS-seq) is not compatible with parallel amplification of RNA and DNA, as DNA methylation is not conserved during in vitro amplification. Single-cell epigenomics approaches utilize chemical treatment of DNA (bisulfite conversion), immunoprecipitation or enzymatic digest (e.g., by DNaseI) to study DNA modifications (scBS-seq and scRRBS), histone modifications (scChIP-seq), DNA accessibility (scATAC-seq, scDNase-seq), chromatin conformation (scDamID, scHiC)

Mentions:
High-throughput sequencing has revolutionized the field of epigenetics with methods for genome-wide mapping of DNA methylation, histone modifications, chromatin accessibility, and chromosome conformation (Table 1). Initially, the input requirements for these methods meant that samples containing hundreds of thousands or millions of cells were required; but in the last couple of years this has changed with numerous epigenetic features now assayable at the single-cell level (Fig. 1). Combined single-cell methods are also emerging that allow analyses of epigenetic–transcriptional correlations thereby enabling detailed investigations of how epigenetic states are associated with phenotype.Table 1

Fig1: Epigenomics and the spectrum of single-cell sequencing technologies. The diagram outlines the single-cell sequencing technologies currently available. A single cell is first isolated by means of droplet encapsulation, manual manipulation, fluorescence-activated cell sorting (FACS) or microfluidic processing. The first examples of single-cell multi-omic technologies have used parallel amplification or physical separation to measure gene expression (scRNA-seq) and DNA sequence (scDNA-seq) from the same cell. Note that single-cell bisulfite conversion followed by sequencing (scBS-seq) is not compatible with parallel amplification of RNA and DNA, as DNA methylation is not conserved during in vitro amplification. Single-cell epigenomics approaches utilize chemical treatment of DNA (bisulfite conversion), immunoprecipitation or enzymatic digest (e.g., by DNaseI) to study DNA modifications (scBS-seq and scRRBS), histone modifications (scChIP-seq), DNA accessibility (scATAC-seq, scDNase-seq), chromatin conformation (scDamID, scHiC)

Mentions:
High-throughput sequencing has revolutionized the field of epigenetics with methods for genome-wide mapping of DNA methylation, histone modifications, chromatin accessibility, and chromosome conformation (Table 1). Initially, the input requirements for these methods meant that samples containing hundreds of thousands or millions of cells were required; but in the last couple of years this has changed with numerous epigenetic features now assayable at the single-cell level (Fig. 1). Combined single-cell methods are also emerging that allow analyses of epigenetic–transcriptional correlations thereby enabling detailed investigations of how epigenetic states are associated with phenotype.Table 1

Bottom Line:
Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation.Here we review available techniques and future possibilities, arguing that the full potential of single-cell epigenetic studies will be realized through parallel profiling of genomic, transcriptional, and epigenetic information.

ABSTRACTEmerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that the full potential of single-cell epigenetic studies will be realized through parallel profiling of genomic, transcriptional, and epigenetic information.